There has been interest in generating hierarchical assemblies of periodic nanoparticle arrays on large-area substrates for a wide range of applications including nanoplasmonics, photochemical catalysts, batteries, photovoltaics, and biological sensors. Studies have focused on the nanoparticle assembly onto a flat surface using techniques such as electron beam lithography, nanoimprint lithography, or block copolymer as lithography mask. However, techniques to fabricate a particle-in-cavity (PIC) nanostructure are lacking despite the advantages of this architecture in many applications.